Gabriel Murta was kicked and slapped by players from lower-league Amantes de Bola, while the manager invaded the pitch demanding a red card, it is claimed.
Murta, said to be a policeman by day, reacted by racing to the changing rooms and returning with a firearm.
Shocking footage captured by a spectator shows a linesman restraining Gabriel Murta as he holds the gun in his hand as he returns to the pitch.
The player thought to have assaulted the referee is seen running off the field as he sees the official storming towards him with the weapon in his hand.
Mr Murta alleges he was kicked and slapped by players from lower-league Amantes de Bola during the first half of the game.
It is understood that the referee reacted by racing to the changing rooms at half time and returning with a firearm.
The incident happened during a regional league match in Brumadinho near Belo Horizonte, Brazil’s sixth largest city and the capital of the state of Minais Gerais.
Brazilian Referees' Association boss Giuliano Bozzano said the official felt threatened and went to look for the weapon to defend himself.
He is due to undergo a psychological assessment and could face suspension or a permanent ban.
